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Emerging infectious diseases (EIDs) are a salient threat to many animal taxa, causing local and global extinctions, altering communities and ecosystem function. The EID chytridiomycosis is a prominent driver of amphibian declines, which is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). To guide conservation policy, we developed a predictive decision-analytic model that combines empirical knowledge of host-pathogen metapopulation dynamics with expert judgment regarding effects of management actions, to select from potential conservation strategies. We apply our approach to a boreal toad (Anaxyrus boreas boreas) and Bd system, identifying optimal strategies that balance tradeoffs in maximizing toad population persistence and landscape-level distribution, while considering costs. The most robust strategy is expected to reduce the decline of toad breeding sites from 53% to 21% over 50 years. Our findings are incorporated into management policy to guide conservation planning. Our online modeling application provides a template for managers of other systems challenged by EIDs.

The effects of contemporary logging practices on headwater stream amphibians have received considerable study but with conflicting or ambiguous results. We posit that focusing inference on specific life stages may help refine understanding, as aquatic and terrestrial impacts may differ considerably. Within a before-after timber harvest experiment, we used recaptures of individually-marked amphibians and a joint probability model of survival, movement, and capture probability, to measure relationships with stream reach, stream gradient, pre- and post-harvest periods, and the timber harvest intensity. Downstream biased movement occurred in both species but was greater for Coastal Tailed Frog (Ascaphus truei) larvae than aquatic Coastal Giant Salamanders Dicamptodon tenebrosus.. For D. tenebrosus, downstream biased movement occurred early in life, soon after an individual?s first summer. Increasing timber harvest intensity reduced downstream movement bias and reduced survival D. tenebrosus but neither of these effects were detected for A. truei larvae. The limited distribution of A. truei among study reaches diminished our ability to measure treatment effects compared to D. tenebrosus.

The reconstruction of US Highway 26/287 over Togwotee Pass, Wyoming, impacted or caused the loss of natural wetlands. To comply with U.S. Army Corps of Engineers permit conditions, the Wyoming Department of Transportation (WYDOT) recently completed construction or restoration of 38 mitigation wetlands along the Highway 26-287 corridor and at the aggregate pit site at the U.S. Forest Service Blackrock Ranger Station. This study provides WYDOT information on differences among wetlands created to mitigate for wetland loss (n=10), wetlands impacted but not destroyed (n=7), and natural wetlands (n=16) relative to various aspects of wildlife that use these habitats. We compare characteristics of amphibians, a pathogenic fungus, invertebrates, and birds. Created wetlands in this study area were significantly shallower than natural and impacted wetlands and had shorter hydroperiods; but impacted wetlands were similar in physical habitat characteristics to natural wetlands. Boreal toads (Anaxyrus boreas) rapidly colonized newly constructed wetlands and annual survival and recruitment rates were similar in created and natural wetlands. Boreal chorus frogs (Pseudacris maculata) were less than half as likely to occupy created wetlands as natural and impacted wetlands but population sizes were high in at least one created wetland. Barred tiger salamanders (Ambystoma mavortium) occurred in natural and impacted wetlands at similar levels, but we observed reproduction by Columbia spotted frogs (Rana luteiventris) at only one created wetland-they were common in natural and impacted wetlands. There was no difference in the prevalence of the pathogenic fungus between created and natural wetlands. Species richness of invertebrates was lower in constructed wetlands than in natural and impacted wetlands and the community composition of invertebrates differed among wetland types. Communities in created wetlands were more likely to be dominated by flying species compared to communities in natural wetlands that had more passive dispersers such as snails and clams. We recorded bird calls in two created and two natural wetlands; species richness was similar but some riparian specialists (e.g., willow flycatcher, Wilson's warbler) were not detected at either created wetland. Our results suggest that wetland creation can be an important tool for conserving wetland-dependent wildlife. Understanding how animals use created wetlands sites is a critical component to understanding the efficacy of mitigation efforts and determining alternative (e.g., earlier) endpoints. This report highlights characteristics in created sites that are advantageous to species that are perhaps non-focal, but important members of the natural community. The data presented here provide support for earlier endpoints for determining success in created wetlands and a baseline for continued monitoring of these or other created sites.

Since the early 1990s, > 5,000 ha of historic wetlands (and adjacent prairie)
have been restored on the row-crop agricultural landscape of Winnebago County, Iowa, USA.
From 2008?2011, we surveyed 22 of these sites for probabilities of occupancy and colonization
by Boreal Chorus Frogs (BCF; Pseudacris maculata), Northern Leopard Frogs (NLF; Lithobates
pipiens), and American Toads (AT; Anaxyrus americanus). We used radio telemetry to measure
patterns of movement and habitat use by 22 NLF and 54 AT, and deployed biophysical models
in available habitats to estimate their physiological costs. BCF occupied 100% of restored
wetlands; NLF and AT occupied 59?91% and 71?89%, respectively, varying according to annual
weather conditions. BCF colonized new sites within a year; NLF and AT required 3 and 2 yr,
respectively.

Drought has fueled an increased frequency and severity of large wildfires in many ecosystems. Despite an increase in research on wildfire effects on vertebrates, the vast majority of it has focused on short-term (<5 yrs) effects and there is still little information on the time scale of population recovery for species that decline in abundance after fire. In 2003, a large wildfire in Montana (USA) burned the watersheds of four of eight streams that we sampled for larval Rocky Mountain tailed frogs (Ascaphus montanus) in 2001. Surveys during 2004?2005 revealed reduced abundance of larvae in burned streams relative to unburned streams, with greater declines associated with increased fire extent. Rocky Mountain tailed frogs have low vagility and have several unusual life-history traits that could slow population recovery, including an extended larval period (4 yrs), delayed sexual maturity (6?8 yrs), and low fecundity (<50 eggs/yr). To determine if abundance remained depressed since the 2003 wildfire, we repeated surveys during 2014?2015 and found relative abundance of larvae in burned and unburned streams had nearly converged to pre-fire conditions within two generations. The negative effects of burn extent on larval abundance weakened >58% within 12 yrs after the fire. We also found moderate synchrony among populations in unburned streams and negative spatial autocorrelation among populations in burned streams. We suspect negative spatial autocorrelation among spatially-clustered burned streams reflected increased post-fire patchiness in resources and different rates of local recovery. Our results add to a growing body of work that suggests populations in intact ecosystems tend to be resilient to habitat changes caused by wildfire. Our results also provide important insights into recovery times of populations that have been negatively affected by severe wildfire.

Emerging infectious diseases such as chytridiomycosis and ranavirus infections are considered important contributors to the worldwide decline of amphibian populations. We reviewed data on 247 anuran mortality events in 43 states of the United States from 1999 ? 2015. Our findings suggest that a severe infectious disease of tadpoles caused by a protist belonging to the phylum Perkinsea might represent the third most common infectious disease of anurans after ranavirus infections and chytridiomycosis. Severe Perkinsea infections (SPI) were systemic and led to multiorganic failure and death. The SPI mortality events affected numerous anuran species and occurred over a broad geographic area, from boreal to subtropical habitats. Livers from all PCR-tested SPI-tadpoles were positive for the Novel Alveolate Group 01 (NAG01) of Perkinsea, while only 2.5% of apparently normal tadpole livers tested positive, suggesting that subclinical infections are uncommon. Phylogenetic analysis demonstrated that SPI is associated with a genetically distinct clade of NAG01 Perkinsea. These data suggest that this virulent Perkinsea clade is an important pathogen of frogs in the United States. Given its association with mortality events and tendency to be overlooked, the potential role of this emerging pathogen in amphibian declines on a broad geographic scale warrants further investigation

The Major Histocompatibility Complex (MHC) is a genomic region encoding immune loci that are important and frequently used markers in studies of adaptive genetic variation and disease resistance. Given the primary role of infectious diseases in contributing to global amphibian declines, we characterized the hypervariable exon 2 and flanking introns of the MHC Class II&#61538; chain for 17 species of frogs in the Ranidae, a speciose and cosmopolitan family facing widespread pathogen infections and declines. We find high levels of genetic variation concentrated in the Peptide Binding Region (PBR) of the exon. Ten codons are under significant positive selection, nine of which are located in the mammal-defined PBR. We hypothesize that the tenth codon (residue 21) is an amphibian-specific PBR site that may be important in disease resistance. Trans-species and trans-generic polymorphisms are evident from exon-based genealogies, and co-phylogenetic analyses between intron, exon and mitochondrial based reconstructions reveal incongruent topologies, likely due to different locus histories. We developed two sets of barcoded adapters that reliably amplify a single and likely functional locus in all screened species using both 454 and Illumina based sequencing methods. These primers provide a resource for multiplexing and directly sequencing hundreds of samples in a single sequencing run, avoiding the labour and chimeric sequences associated with cloning, and enabling MHC population genetic analyses. Although the primers are currently limited to the 17 species we tested, these sequences and protocols provide a useful genetic resource and can serve as a starting point for future disease, adaptation and conservation studies across a broad range of Ranid taxa.

Over 2 years of surveys of 3 stream networks, stream salamander occupancy was better described by covariates related to the position of the site within the network than microhabitat features. Via simulation, we found that changes in occupancy can be detected by preferentially sampling headwaters, but causes of variation in extinction rates will require more intensive effort.

1. Conservation science can be most effective in its decision-support role when seeking answers to clearly formulated questions of direct management relevance. Emerging wildlife diseases, a driver of global biodiversity loss, illustrate the challenges of performing this role: in spite of considerable research, successful mitigation remains uncommon. Decision analysis is increasingly advocated to guide mitigation planning, but its application remains uncommon.
2. Using an integral projection model, we explored potential mitigation actions for avoiding population declines and the ongoing spatial spread of the fungus Batrachochytrium salamandrivorans (Bsal). This fungus has recently caused severe amphibian declines in north-western Europe and threatens Palearctic salamander diversity.
3. Available evidence suggests that a Bsal outbreak in a fire salamander (Salamandra salamandra) population will lead to its rapid extirpation. Treatments such as antifungals or probiotics would need to almost entirely interrupt transmission (reduce probability of infection by more than 90%) to avert host extirpation and successfully eradicate the pathogen.
4. Improving the survival of infected hosts is most likely to be detrimental as it increases the potential for pathogen transmission and dispersal. Active removal of host species has some potential to reduce the spread of Bsal, but its effectiveness depends on the presence of Bsal reservoirs and on the host?s spatial dynamics, which should therefore represent research priorities.
5. Synthesis and applications. Mitigation of Bsal epidemics in susceptible host species is highly unlikely, requiring highly efficient interruption of transmission and substantial removal of host individuals. More in general, our study illustrates the advantages of framing conservation science directly in the management decision context, rather than adapting to it a posteriori.

Here, we report the first instances of Pacific boas (Candoia bibroni) eating amphibians in the wild. Specifically, we documented Cornufer vitianus (Fiji Ground Frog) and C. vitiensis (Fiji Tree Frog), both formerly in the genus Platymantis (for taxonomic discussion see Brown et al. 2015. Zool. J. Linn. Soc-Lond. 174:130?168), as prey for the first time.

From 2002-2006, we used a variety of sampling techniques to survey the amphibians and water chemistry of Lower Suwannee National Wildlife Refuge in Florida?s Big Bend region. We recorded 23 amphibian species, 19 frogs and 4 salamanders. Species richness was lower than in areas of the coastal Big Bend region to the north, perhaps due to a combination of variation in the geographic range of different amphibian species? ranges, sampling techniques, times of year when sampling occurred, and variation in detection probabilities among years and regions. Amphibians occupied a wide variety of habitats and appeared tolerant of the generally acidic conditions of many of the wetlands. Small streams and the Suwannee River were less acidic and had greater conductivities and mineral concentrations than isolated ponds; concentrations of heavy metals varied and mercury was not detected. Although additional species may yet be found in LSNWR, this survey provides a historic baseline for assessing future status and trends of amphibian populations as areas adjacent to the refuge are disturbed and as restoration and multi-use management continue within its boundaries.

Managers are increasingly implementing reintroduction programs as part of a global effort to alleviate amphibian declines. Given uncertainty in factors
affecting populations and a need to make recurring decisions to achieve objectives, adaptive management is a useful component of these efforts. A
major impediment to the estimation of demographic rates often used to parameterize and refine decision-support models is that life-stage-specific
monitoring data are frequently sparse for amphibians. We developed a new parameterization for integrated population models to match the ecology of amphibians and capitalize on relatively inexpensive monitoring data to document amphibian reintroductions. We evaluate the capability of this
model by fitting it to Oregon spotted frog (Rana pretiosa) monitoring data collected from 2007 to 2014 following their reintroduction within the Klamath Basin, Oregon, USA. The number of egg masses encountered and the estimated adult and metamorph abundances generally increased following reintroduction. We found that survival probability from egg to metamorph ranged from https://0.01 in 2008 to https://0.09 in 2009 and was not related to minimum spring temperatures, metamorph survival probability ranged from https://0.13 in 2010-2011 to https://0.86 in 2012-2013 and was positively related
to mean monthly temperatures (logit-scale slope = 2.37), adult survival probability was lower for founders (0.40) than individuals recruited after
reintroduction (0.56), and the mean number of egg masses per adult female was https://0.74. Our study represents the first to test hypotheses concerning Oregon spotted frog egg-to-metamorph and metamorph-to adult transition probabilities in the wild and document their response at multiple life stages following reintroduction. Furthermore, we provide an example to illustrate how the structure of our integrated population model serves as a useful foundation for amphibian decision-support models within adaptive management programs. The integration of multiple, but related, datasets has an advantage of being able to estimate complex ecological relationships across multiple life stages, offering a modeling framework that accommodates uncertainty, enforces parsimony, and ensures all model parameters can be confronted with monitoring data.

1. The amphibian skin microbiome is recognized for its role in defense against pathogens, including the deadly fungal pathogen Batrachochytrium dendrobatidis (Bd). Yet, we have little understanding of evolutionary and ecological processes that structure these communities, especially for salamanders and closely related species. We investigated patterns in the distribution of bacterial communities on Plethodon salamander skin across host species and environments.
2. Quantifying salamander skin microbiome structure contributes to our understanding of how host-associated bacteria are distributed across the landscape, among host species, and their putative relationship with disease.
3. We characterized skin microbiome structure (alpha-diversity, beta-diversity and bacterial operational taxonomic unit [OTU] abundances) using 16S rRNA gene sequencing for co-occurring Plethodon salamander species (3571 P. cinereus, 17 P. glutinosus, 10 P. cylindraceus) at three localities to differentiate the effects of host species from environmental factors on the microbiome. We sampled the microbiome of P. cinereus along an elevational gradient (n = 50, 700 ? 1000 masl) at one locality to determine whether elevation predicts microbiome structure. Finally, we quantified prevalence and abundance of putatively anti-Bd bacteria to determine if Bd-inhibitory bacteria are dominant microbiome members.
4. Co-occurring salamanders had similar microbiome structure, but among sites salamanders had dissimilar microbiome structure for beta-diversity and abundance of 28 bacterial OTUs. We found that alpha-diversity increased with elevation, beta-diversity and the abundance of 17 bacterial OTUs changed with elevation (16 OTUs decreasing, 1 OTU increasing). We detected 11 putatively anti-Bd bacterial OTUs that were present on 90% of salamanders and made up an average relative abundance of 83% (SD ? 8.5) per salamander. All salamanders tested negative for Bd.
5. We conclude that environment is more influential in shaping skin microbiome structure than host differences for these congeneric species, and suggest that environmental characteristics that co-vary with elevation influence microbiome structure. High prevalence and abundance of anti-Bd bacteria may contribute to low Bd levels in these populations of Plethodon salamanders.

The California red-legged frog Rana draytonii has been declining across its native range since the 1960s and was considered extirpated from most of southern California. In February 2017, a population of R. draytonii was re-discovered in the San Bernardino Mountains of Riverside County, California, where it has not been documented since 1959 (LACM 91074). This population belongs to a mtDNA lineage thought to be extinct from this species within the United States but still extant in Mexican populations. This discovery increases the potential for future, evolutionarily-informed translocations within the southern portion of this species range in California.

This paper summarizes the results of Bd and Bsal testing of 76 Gulf Coast Waterdogs captured from southeast Louisiana.

As the spatial and temporal scale of ecological research expands, there is increasing need for methods that integrate multiple data types into a single analytical framework. Current work on this topic primarily focuses on combining capture-recapture data from marked individuals with other data types into integrated population models. Yet, studies of species distributions and trends often rely on data from unmarked individuals across broad scales where local abundance and environmental variables may vary. We present a modeling framework for integrating detection/nondetection and count data into a single analysis to estimate population dynamics, abundance, and individual detection probabilities during sampling. Our dynamic population model assumes that site-specific abundance can change over time according to survival of individuals and gains through reproduction and immigration. The observation process for each data type is modeled by assuming that every individual present at a site has an equal probability of being detected during sampling processes. We examine our modeling approach through a series of simulations illustrating the relative value of count versus detection/nondetection data under a variety of parameter values and survey configurations. We also provide an empirical example of the model by combining long-term detection/nondetection data (1995-2014) with newly collected count data (2015-2016) from a growing population of barred owls (Strix varia) in the Pacific Northwest to examine the factors influencing population abundance over time. Our model provides a foundation for incorporating unmarked data within a single framework, even in cases where sampling processes yield different detection probabilities. This approach will be useful for survey design and to researchers interested in incorporating historical or citizen science data into analyses focused on understanding how demographic rates drive population abundance.

Although not yet detected in the United States, the emergence of Bsal (a fungal pathogen) could threaten the salamander population, which is the most diverse in the world. The spread of Bsal likely will lead to more State and federally listed threatened or endangered amphibian species, and associated economic effects. Because of concern expressed by resource management agencies, the U. S. Geological Survey has made Bsal and similar pathogens a priority for research.

Diverse bacteria inhabit amphibian skin, some of which inhibit growth of the fungal pathogen, Batrachochytrium dendrobatidis (Bd). Yet, there has been no systematic survey of anti-Bd bacteria across localities, species and elevations. This is important given geographic and taxonomic variation in amphibian susceptibility to Bd. Our sites were within the Appalachian Mountains where previous sampling indicated low Bd prevalence. We determined the number and identity of anti-Bd bacteria on 61 Plethodon salamanders (37 P. cinereus, 15 P. glutinosus, 9 P. cylindraceus) using culturing methods and 16S rDNA sequencing. We sampled co-occurring species at three localities, and P. cinereus along an elevational gradient (700 ? 1000 masl) at one locality. We identified 50 anti-Bd bacterial OTUs and found that the degree of Bd inhibition was not correlated with relatedness. Five anti-Bd bacteria occurred on multiple species at multiple localities, but none were shared among all species and localities. Prevalence of
36 anti-Bd bacteria was higher at Shenandoah NP, VA, with 96% (25/26) of salamanders hosting at least one anti-Bd bacteria compared to 50% (7/14) at Catoctin MP, MD and 38% (8/21) at Mt. Rogers NRA, VA. At the individual level, salamanders at Shenandoah NP had more anti-Bd bacteria per individual (&#956; = 3.3) than those at Catoctin MP (&#956; = 0.8) and at Mt. Rogers NRA (&#956; = 0.4). All salamanders tested negative for Bd. Anti-Bd bacteria are diverse in central Appalachian Plethodon salamanders, and their distribution varied geographically. The antifungal bacteria we identified may play a protective role for these salamanders.

Our work is motivated by the impacts of the emerging infectious disease chytridiomycosis, a disease of amphibians that associated with declines of many species worldwide. Using this host-pathogen system as a general example, we first illustrate how misleading inferences can result from failing to incorporate pathogen dynamics into the modeling process, especially when the pathogen is difficult or impossible to survey in the absence of a host species. We found that traditional modeling techniques can underestimate the effect of a pathogen on host species occurrence and dynamics when the pathogen can only be detected in the host, and pathogen information is treated as a covariate. We propose a dynamic multistate modeling approach that is flexible enough to account for the detection structures that may be present in complex multistate systems, especially when the sampling design is limited by a species’ natural history or sampling technology.